Hybridization Capture Results.

Samples are described in detail in Table S1. The E. coli sample was captured with five 1 kb E. coli specific baits (Capture), was shotgun sequenced (shotgun) or captured with a bait representing the koala retrovirus genome (KoRV). The rodent dilution series are indicated by respective concentration of input library used in each capture experiment (see also Fig. 1). Genome indicates the full genome size for bacterial and mitochondrial genomes respectively. Bait indicates the total unsheared length of the target sequence PCR product used to capture from the libraries. Total reads indicates the total usable high quality sequence reads obtained. Target reads indicate those reads mapping to the targeted region only which is also given as a percent on-target. The percentage of reads mapping to specific genomes, bacterial or mitochondrial, are indicated as % flank reads. The % unspecific reads are those that neither mapped to the target sequence nor to the genome to which the target belongs. Bait fold indicates the fold enrichment of the targeted region (covered by the bait). The flank fold indicates the fold enrichment of sequences flanking the bait. The total fold coverage is an average of the bait specific and flanking region coverage. The % zero coverage indicates the percentage of the targeted genomes that had no sequence read coverage.The shotgun sequences are given as fold enrichment of specific target sequences as a comparison to the hybridization capture results. However, no enrichment took place for the shotgun sequencing.aBaits sheared or generated by PCR such that individual fragments range in length from 200–500 bp.bThe koala samples were captured with mixed target baits and thus NA indicates that the statistics for these samples are not applicable. Percent of genome with zero coverage was not calculated for the museum samples as CapFlank was shown to only extend minimally in these samples (Figure 2).Hybridization Capture Results.